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- PDB-4eyt: Crystal structure of the C-terminal domain of Tetrahymena telomer... -

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Basic information

Entry
Database: PDB / ID: 4eyt
TitleCrystal structure of the C-terminal domain of Tetrahymena telomerase protein p65
ComponentsTelomerase associated protein p65
KeywordsRNA BINDING PROTEIN / RNA / LA protein / LARP7 / RRM / xRRM
Function / homology
Function and homology information


telomerase catalytic core complex assembly / telomerase RNA stabilization / telomerase holoenzyme complex / telomerase RNA binding / telomere maintenance via telomerase / chromosome, telomeric region
Similarity search - Function
La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
La-related protein 7 homolog / La-related protein 7 homolog
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSingh, M. / Wang, Z. / Koo, B.-K. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
CitationJournal: Mol.Cell / Year: 2012
Title: Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65.
Authors: Singh, M. / Wang, Z. / Koo, B.K. / Patel, A. / Cascio, D. / Collins, K. / Feigon, J.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomerase associated protein p65
B: Telomerase associated protein p65
C: Telomerase associated protein p65
D: Telomerase associated protein p65
E: Telomerase associated protein p65
F: Telomerase associated protein p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9667
Polymers93,8706
Non-polymers961
Water18010
1
A: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)15,6451
Polymers15,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Telomerase associated protein p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7412
Polymers15,6451
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)15,6451
Polymers15,6451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)15,6451
Polymers15,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)15,6451
Polymers15,6451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Telomerase associated protein p65


Theoretical massNumber of molelcules
Total (without water)15,6451
Polymers15,6451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.190, 91.900, 82.830
Angle α, β, γ (deg.)90.000, 107.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Telomerase associated protein p65


Mass: 15645.020 Da / Num. of mol.: 6 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP65 / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6JXI6, UniProt: W7X6T2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN CONSTRUCT COMPRISES THE C-TERMINAL XRRM2 DOMAIN OF P65 (UNP RESIDUES 375-542) WITH THE LOOP ...PROTEIN CONSTRUCT COMPRISES THE C-TERMINAL XRRM2 DOMAIN OF P65 (UNP RESIDUES 375-542) WITH THE LOOP (UNP RESIDUES 413-459) DELETED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M phosphate/citrate, 0.2 M lithium sulfate, 20% w/v PEG1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→79.057 Å / Num. all: 38820 / Num. obs: 36719 / % possible obs: 94.5 % / Redundancy: 6.2 % / Rsym value: 0.085 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.50.5771.31827252760.57793.5
2.64-2.83.60.4041.91826450290.40493.9
2.8-2.9970.5441.23317447380.54494.4
2.99-3.237.30.3451.93237044140.34594.7
3.23-3.547.40.17143009740890.17194.4
3.54-3.9570.1324.32615837210.13295.1
3.95-4.567.30.0669.52401432680.06694.9
4.56-5.597.40.0629.42067728060.06295.5
5.59-7.917.30.05411.41572021510.05495.4
7.91-60.5496.30.02820.2768212270.02894.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ERD

4erd


Resolution: 2.5→60.549 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7388 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.91 / Phase error: 32.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1845 5.02 %RANDOM
Rwork0.2247 ---
obs0.2269 36715 92.94 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.567 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 204.87 Å2 / Biso mean: 93.5003 Å2 / Biso min: 38.87 Å2
Baniso -1Baniso -2Baniso -3
1-2.4752 Å2-0 Å2-0.9894 Å2
2--0.1246 Å2-0 Å2
3----2.5998 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 5 10 4925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094997
X-RAY DIFFRACTIONf_angle_d1.1926726
X-RAY DIFFRACTIONf_chiral_restr0.082727
X-RAY DIFFRACTIONf_plane_restr0.004875
X-RAY DIFFRACTIONf_dihedral_angle_d16.2661913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.53420.41991470.36712545269289
2.5342-2.57040.45381590.36642627278690
2.5704-2.60880.37591050.35452595270090
2.6088-2.64960.35811410.34342684282592
2.6496-2.6930.44621540.32712628278291
2.693-2.73950.36771490.31832689283893
2.7395-2.78930.36221660.30882624279092
2.7893-2.84290.38041630.29442642280593
2.8429-2.90090.3591100.28752680279093
2.9009-2.9640.29211180.27242713283193
2.964-3.0330.38461400.27092752289294
3.033-3.10880.35891390.29132714285394
3.1088-3.19290.32111400.26482672281293
3.1929-3.28680.33471380.23692683282194
3.2868-3.39290.26141740.23992658283293
3.3929-3.51410.272960.24192799289594
3.5141-3.65480.29361780.25992680285894
3.6548-3.82110.30161420.28272684282694
3.8211-4.02260.28981290.2052703283294
4.0226-4.27450.22461260.17392769289594
4.2745-4.60450.19541310.142754288594
4.6045-5.06760.19411380.14972710284894
5.0676-5.80040.22761380.20442727286595
5.8004-7.30590.28831660.23762735290195
7.3059-60.56630.21631660.21092688285494
Refinement TLS params.Method: refined / Origin x: 27.7567 Å / Origin y: -32.7516 Å / Origin z: -7.7027 Å
111213212223313233
T0.318 Å20.0045 Å2-0.0307 Å2-0.1418 Å20.0472 Å2--0.6998 Å2
L1.6595 °20.1181 °20.5263 °2-1.3383 °20.0599 °2--0.6243 °2
S0.1152 Å °0.0221 Å °-0.2074 Å °-0.1071 Å °-0.0338 Å °-0.3873 Å °0.0209 Å °0.0388 Å °-0.0523 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA376 - 603
2X-RAY DIFFRACTION1allC377 - 522
3X-RAY DIFFRACTION1allB378 - 704
4X-RAY DIFFRACTION1allE378 - 522
5X-RAY DIFFRACTION1allD378 - 603
6X-RAY DIFFRACTION1allF378 - 522

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